In the early 1900's, a dark shadow covered a small country town in rural America. At that time, a young married couple vanished mysteriously from their home.

The man's name was George, The woman's name was Maria.Two years later, as suddenly as he left, George returned. He never told anyone where he had been or what he had done. But, he began an odd study, all by himself.As for Maria, his wife... She never returned.

Mother starts 80 years after the vanishing of George and his wife Maria.
You play as Ninten the great-grandchild of George in the beginning,
and must stop an evil extra-terrestrial power that is abducting the people.
With friends that you find on the way, and the powers you gain with hardship.

The game starts with Ninten's house under attack by a poltergeist. The ghost is possessing objects in Ninten's house, like a lamp, and a doll. Obviously, he has no choice but to defeat them. Afterwards, he contacts his father who tells him to open the locked door to the basement. Ninten does so, after getting the key from his dog. Inside, he finds his great-grandfather's diary. Afterwards, Ninten sets out on a grand adventure.

Ninten talks to the mother of his neighbour, Pippi. She says that Pippi has gone missing! She also asks you to talk to the mayor about it. As you do so, he asks you to rescue Pippi in order to secure his reinstatement as mayor. Ninten heads to the cemetery to find Pippi.

After finding a mysterious hole, Ninten enters it. Inside are a flight of stairs that leads to a room with four coffins. One of them holds Pippi. After Ninten finds the coffin, Pippi goes with him to meet the mayor. After leaving Pippi with the mayor, Ninten goes to the zoo to investigate the cause of rogue animals. As he approaches the gate, a monkey guards the way. He shows the monkey the key, and the monkey runs of with it. Ninten examines the area of the zoo, and finds the administrator's office. Inside, he sees a glowing capsule. This capsule, once examined, turns into a Starman. Ninten promptly defeats the PSI-wielding alien.

Afterwards, the road to Merryville is guarded by police officers. Talk to them and they will allow you to pass. Although what you find at the end of the path isn't a city, instead it's a cave with an oddly shaped stone. After Ninten uses his Great-Grandfather's diary to answer it's riddle, he is teleported to Magicant.

Magicant is a city of odd people, including Swimming Cats, Flying Men, and other odd creatures. Ninten hears talk of a Queen of Magicant. He heads towards her castle, using Telepathy on her guards to answer their riddle. Ninten meets with her, and Mary asks him to sing to him the Eight Melodies once complete. Ninten is happy to do so, and leaves. Although after some searching, he finds there is no way out of Magicant. What do you do? Head for something that looks suspicious. Like a hole in the ground.

Ninten finds many holes in the ground south-east of Mary's castle. Once he finds one he can enter, he does so. After wandering around the maze-like area, he finds the Onyx Hook, which allows him to enter Magicant anytime. He leaves after speaking constantly to the exit-guarder.

Ninten arrives south of Merryville. He heads towards the town, and they speak of Duncan's Factory. If you enter the school, however, they speak of Loid and how he stole Bottle Rockets. After Ninten is allowed to enter the locked roof, he meets Loid, hiding in a garbage can. He asks Ninten for some Bottle Rockets. Ninten fetchs some from a nearby factory. Afterwards, Loid joins Ninten.

Now, the duo head for the train by Merryville. Unfortunately, rocks block the way. Fortunately, there is talk of Duncan's Factory, a factory that specializes in explosives. Think an explosion could clear the rocks? Go find out! Ninten and Loid head for Duncan's Factory.

Inside the factory, there is lots of space, and powerful enemies. Ninten and Loid persevere and fire the rocket at the end of the factory. The rocket hits it's target and destroys the rocks. Ninten and Loid now head for Reindeer. There, a woman in the station gives Ninten a hat with the name Ana. Ana is found in Snowman. After Ninten gives her the hat, she joins Ninten and Loid. They now head to Spookane. There, Ninten and company sleep inside the hotel in the southern area of the town. After the night, a Starman attacks. The group fends off this monster from the stars. Now, they head to the residential district.

Ninten's group sees everyone outside. Apparently, ghosts have invaded their homes, similar to Podunk's situation earlier in the game. A woman gives Ninten the key to the Rosemary Manor, which is believed to be the source of the invading. The theory is correct, as the trio finds the piano that is controlling the ghosts, it plays a melody which is another part of the song. They leave Spookane via the train station to Union Station and head east to a broken bridge but they find a way around and enter the Yucca Desert where bones talk about how boring it is here, Ninten and friends tread through the vast desert, struggling against powerful monsters and dehydration to an oasis, Nearby a man is here and seems to be a war veteran from a war that waged here in Yucca desert years ago, he offers them tours of the desert in his plane giving them ticket stubs, when Ninten and co. tour around they find an odd cactus which they approach on foot, It speaks into Ninten's mind and uses telepathy which he then obtains the fifth melody. He then finds a land mine in the desert instead of exploding however, he recieves a Message from Shigesato Itoi the game's producer.

When they obtain 10 ticket stubs, the veteran keeps his word and lends them his tank Ninten and co. uses it to get to old ruins, when they do they find a giant robot known as R7037 it attacks them but due to the tank they easily beat the colossus...and destroy the tank at the same time...At this point they enter the ruins.

Apon descending the ladder they arrive at the Monkey grotto where mokeys live and are credited as famed liars, They get out and find another gate to Magicant.

They return to the Dragon sleeping in Crystal Caverns, feeling Ninten's stronger than ever presence he awakens and attacks them, After defeating the dragon it croons out the sixth melody, Ninten leaves magicant once again picking up a sword along the way.

They find themselves at a new exit gate outside they find out that they are south of Yucca Desert, they walk east, following the train tracks and head for Youngtown, at the station a man is there but too nervous to repair some broken train tracks then Ninten walks southwest to Youngtown.

At Youngtown's gate they find a child guarding it they learn their stories about all the resident's parents were abducted, which is similar to Ana's situation they walk around and learn of a baby with odd abilities, they find the baby in the Garrickson's household, Ninten, with the urge to find out about this mystic power tries to communicate with the baby but alas it has not learned how to speak so they communicate with Telepathy, The baby then presents them with the power of teleportation. (Note: This baby (although still under debate) is possibly a young infant Ness).

At the Eastmost point of Youngtown they find a sign that points to a nearby swamp, they enter it and brave the new powerful adversaries and reach a lone house with a wriggling garbage can next to it, inside is Loid's father (Ironic) and asks you for your name...Your name.
Inside the House is someone you would never expect to see: The all Powerful Pippi! all the way from Podunk she lets you rest there for free, take advantage of the situation and train around the swamp, things will only get worse. when they start encountering Buffalos it's a sign Ellay is close.

At Ellay the group encounters the notorious Bla Bla Gang and finds a place with live singing they need tickets so they buy some from the department store but yet again another problem surfaces, The veteran is blocking the entrance demanding a small amount of money in compensation for his broken tank (Not really much considering how much of a help it was), inside they are offered alcohol but refusal is a must, they are then asked to dance on stage and afterwards the Leader of the Bla bla gang comes out and confronts you for beating his allies, this battle will be finished in roughly three rounds, seriously.

After battle he introduces himself as Teddy and commends you as a powerful trio of fighters and talk about his long lost parents and wanting revenge on the meanie who did this to him, which convieniently for us, he knows where he is:Mt. Itoi The most broken dungeon in all of gaming. He'll join your party replacing Loid in every single way taking his items too.
He's a good powerhouse, a nice ally to join your side.

They then approach Mt. Itoi. The trio climb through the mountain and reach the first summit where they find a healer's house. When the group try to enter the second room of the house Teddy stays in the first saying he's going to make a few phone calls. Ana and Ninten dance, Ana then asks Ninten if he loves her. After he replies Teddy walks into the room and when they try to leave they get attacked by the R7038, an unbeatable boss. When you get beat the robot is hit but so are Ninten, Ana and Teddy.

Loid arrives in a tank revealing that he was the one who fired it, but he missed, he then carries them back to the healers house, Teddy is too injured to carry on so Loid rejoins you in his place. They go past the house and find a boat and ride it thanks to Loid, but get sucked into a whirlpool. They find a labaratoy-like are with a robot in it.

The Robots name is Eve and it was built by George, Ninten's Grandpa, to protect them in their journey. It protects them from a flood which demonstrates her skills. (she is the strongest party member in the game) When they reach a certain point they get attacked by R7038XX. Eve Protects them then explodes to win the fight. But that meant she was gone.

The group examine the wreckage and the seventh melody plays. They continue up the mountain and find a stone with XX writen on it and examine and find out the melody was Nintens Great Grandmothers love and find the final melody.

They reurn to the Queen of Magicant, Queen Mary, to show her the whole song. She then said she loved Gigue but how he hated when she tried to sing him a lulaby. She then reveals she was Maria and goes to join George in the afterlife now her purpose was complete and vanishes, along with Magicant, they are warped back to the XX stone and continue to the summit, they find a room where all the adults from Youngtown are held. They tell them to destroy the mothership. They continue on to boss' lair